Hello Conrad,
thank you for your reply. Attached is a test file that is causing
problems in ChimeraX (see below for the log). This testfile is a
cut-down version of the original file (containing informations on
docking scores from GOLD suite) that was created in Chimera by
saving it as mol2 file and manually removing the zeros in line
8, as Chimera was sanitizing this line upon saving. If I add
the two zeros in the original file, ChimeraX was loading the
structures successfully, still complaining about the
metainformations though.
I'm using version 0.9 (2019-03-12) of Chimera X on Win10
(1809) and was using Chimera 1.13.1 to generate the testfile.
Thank you and best regards,
Marco
| Summary of feedback from opening C:\Users\Marco\Desktop\benzotriazol\chimeratest.mol2 | |
|---|---|
| warnings | line 8: bad
molecule data line 8: ignore unexpected line '57 62 1' line 9: ignore unexpected line 'SMALL' line 10: ignore unexpected line 'USER_CHARGES' |
Opened chimeratest.mol2 containing 0 structures (0 atoms, 0 bonds)
Hi, Marco.
Can you send me the file that is causing the problem? When I change a working Mol2 file to remove those two fields, I get a few error messages but the molecules are opened. I'm concerned that some other error is preventing import of your file.
Conrad
On 3/13/2019 2:23 AM, Marco J. Müller wrote:
Dear ChimeraX Team,
when I try to load structure outputs of docking runs in .mol2 format into ChimeraX, it fails to load them, while the same can be imported by Chimera successfully. After a bit of playing around I found that the following section is relevant and fails in this format:
@<TRIPOS>MOLECULE
MYCOOLMOLECULE
57 62 1
SMALL
USER_CHARGES
The problem seems to be that ChimeraX requires explicit definitions of /#features/ and/#sets/ in the third line (apart from /#atoms #bonds #substructures/), while they are typically omitted in most programs. So the following lines could be imported:
@<TRIPOS>MOLECULE
MYCOOLMOLECULE
57 62 1 0 0
SMALL
USER_CHARGES
Can this case be addressed in a future version of ChimeraX?
Thank you in advance,
Marco
--
Marco J. Müller
PhD student
Technische Universität Braunschweig
Institute of Medicinal and Pharmaceutical Chemistry
https://www.tu-bs.de/pharmchem
Beethovenstr. 55 | 38106 Braunschweig | Germany
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-- Marco J. Müller Technische Universität Braunschweig Institut für Medizinische und Pharmazeutische Chemie https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany Tel.: +49 531 391 2768 | marco.mueller@tu-bs.de